Nucleosides, Nucleotides & Nucleic Acids最新文献_第7页

Identification of exon regions in eukaryotes using fine-tuned variational mode decomposition based on kurtosis and short-time discrete Fourier transform. 利用基于峰度和短时离散傅立叶变换的微调变异模式分解技术识别真核生物中的外显子区域。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-08-10 DOI: 10.1080/15257770.2024.2388785

K Jayasree, Malaya Kumar Hota, Atul Kumar Dwivedi, Himanshuram Ranjan, Vinay Kumar Srivastava

{"title":"Identification of exon regions in eukaryotes using fine-tuned variational mode decomposition based on kurtosis and short-time discrete Fourier transform.","authors":"K Jayasree, Malaya Kumar Hota, Atul Kumar Dwivedi, Himanshuram Ranjan, Vinay Kumar Srivastava","doi":"10.1080/15257770.2024.2388785","DOIUrl":"10.1080/15257770.2024.2388785","url":null,"abstract":"In genomic research, identifying the exon regions in eukaryotes is the most cumbersome task. This article introduces a new promising model-independent method based on short-time discrete Fourier transform (ST-DFT) and fine-tuned variational mode decomposition (FTVMD) for identifying exon regions. The proposed method uses the N/3 periodicity property of the eukaryotic genes to detect the exon regions using the ST-DFT. However, background noise is present in the spectrum of ST-DFT since the sliding rectangular window produces spectral leakage. To overcome this, FTVMD is proposed in this work. VMD is more resilient to noise and sampling errors than other decomposition techniques because it utilizes the generalization of the Wiener filter into several adaptive bands. The performance of VMD is affected due to the improper selection of the penalty factor (α), and the number of modes (K). Therefore, in fine-tuned VMD, the parameters of VMD (K and α) are optimized by maximum kurtosis value. The main objective of this article is to enhance the accuracy in the identification of exon regions in a DNA sequence. At last, a comparative study demonstrates that the proposed technique is superior to its counterparts.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"507-530"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141913462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

miR-146a rs2910164 (G/C) variant may predict morbid obesity risk in adults. miR-146a rs2910164 (G/C) 变异可预测成人病态肥胖风险。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-08-20 DOI: 10.1080/15257770.2024.2393323

Zeki Ozsoy, Ayse Feyda Nursal, Seyma Ozsoy, Akin Tekcan, Serbulent Yigit

{"title":"miR-146a rs2910164 (G/C) variant may predict morbid obesity risk in adults.","authors":"Zeki Ozsoy, Ayse Feyda Nursal, Seyma Ozsoy, Akin Tekcan, Serbulent Yigit","doi":"10.1080/15257770.2024.2393323","DOIUrl":"10.1080/15257770.2024.2393323","url":null,"abstract":"Obesity is a common public health problem associated with serious, life-threatening complications. MicroRNAs (miRs) have modulating roles in the immune and inflammatory systems. Therefore, this study aimed to analyze the relationship between miR-146a and morbid obesity (MO) in a Turkish population. In this study, a total of 258 subjects (110 patients with MO and 148 controls) were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to analyze miR-146a rs2910164. Then, we examined the patients as males and females separately. The results of the analyses were evaluated for statistical significance. There was a significant difference in genotype and allele frequencies of miR-146a rs2910164 between patients with MO and control individuals. miR-146a rs2910164 CC genotype and C allele were shown to increase in the MO patients' group compared to the control group (p = 0.000, p = 0.000, respectively). Also, the C allele was higher in both female and male patients compared to controls (p = 0.000, p = 0.000, respectively). High differences were also observed when the patients and the controls were compared according to CC versus GG + GC and GG versus GC + CC (p = 0.000, p = 0.000, respectively). A significant difference was found between the female/male patients and the female/male controls in terms of GG + GC versus CC (p = 0.000, p = 0.000, respectively). To the best of our knowledge, this is the first study to investigate the relationship between this variant and MO in Turkey. Our results showed that miR-146a rs2910164 is a valuable biomarker that can be used to distinguish between patients with MO and the healthy population. The findings can be extended by increasing the sample sizes with diverse ethnicities.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"653-663"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DNA nanotechnology for cell-free DNA marker for tumor detection: a comprehensive overview. 用于肿瘤检测的无细胞 DNA 标记的 DNA 纳米技术：全面概述。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-10-02 DOI: 10.1080/15257770.2024.2337853

Sara Sami Soliman, Fathi E Abd El-Samie, Saied M Abd El-Atty, Wael Badawy, Abeer Eshra

{"title":"DNA nanotechnology for cell-free DNA marker for tumor detection: a comprehensive overview.","authors":"Sara Sami Soliman, Fathi E Abd El-Samie, Saied M Abd El-Atty, Wael Badawy, Abeer Eshra","doi":"10.1080/15257770.2024.2337853","DOIUrl":"10.1080/15257770.2024.2337853","url":null,"abstract":"Advancements in DNA nanotechnology have led to new exciting ways to detect cell-free tumor biomarkers, revolutionizing cancer diagnostics. This article comprehensively reviews recent developments in this field, discussing the significance of liquid biopsies and DNA nanomachines in early cancer detection. The accuracy of cancer diagnosis at its early stages is expected to be significantly improved by identifying biomarkers. Liquid biopsies, offering minimally-invasive testing, hold the potential for capturing tumor-specific components like circulating tumor cells, cell-free DNA, and exosomes. DNA nanomachines are advanced molecular devices that exploit the programmability of DNA sequences for the ultrasensitive and specific detection of these markers. DNA nanomachines, nanostructures made of DNA that can be designable and switchable nanostructures, have a wide range of advantages for detecting tumor biomarkers, including non-invasiveness, affordability, high sensitivity, and specificity. Scientists also work on dealing with challenges like low marker concentrations and interference, which are addressed through microfluidic integration, nanomaterial amplification, and indirect signal detection. Despite advances, multiplex detection remains a challenge. In conclusion, DNA nanomachines bear immense promise for cancer diagnostics, advocating personalized treatment and improving patient outcomes. Continued research could redefine how we find and treat tumors, leading to better patient outcomes.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"276-290"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effect of human epididymis protein 4 on hyperoxia-induced bronchial dysplasia in newborn rats. 人类附睾蛋白 4 对高氧引起的新生大鼠支气管发育不良的影响

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-07-14 DOI: 10.1080/15257770.2024.2356208

Xiaofang Yan, Xing Feng, Yan Gao, Dawei Liu, Lin Bai, Lu Xu

{"title":"Effect of human epididymis protein 4 on hyperoxia-induced bronchial dysplasia in newborn rats.","authors":"Xiaofang Yan, Xing Feng, Yan Gao, Dawei Liu, Lin Bai, Lu Xu","doi":"10.1080/15257770.2024.2356208","DOIUrl":"10.1080/15257770.2024.2356208","url":null,"abstract":"Objective: The study aimed to elucidate the role and the underlying mechanism of human epididymis protein 4 (HE4) in the pathogenesis of hyperoxia-induced bronchial dysplasia in newborn rats.Methods: Forty neonatal Sprague-Dawley (SD) rats were separated into two groups: a normal control group (20.8% oxygen concentration) and a hyperoxia-induced group (85% oxygen concentration). Three time intervals of 24 h, 3 days and 7 days were chosen for each group. Haematoxylin-eosin staining was used to identify the pathological alterations in the lung tissue of the SD rats. Enzyme-linked immunosorbent assay was used to evaluate plasma protein levels. Real-time reverse transcription polymerase chain reaction was used to determine messenger RNA (mRNA) expression.Results: In newborn SD rats, hyperoxia intervention within 7 days may result in acute lung damage. In the plasma and tissue of newborn SD rats, hyperoxia induction may raise levels of HE4, matrix metalloproteinases (MMP) 9 and tissue inhibitors of metalloproteinases (TIMP) 1. We discovered that the HE4 protein activates the phosphorylation of extracellular regulated protein kinases (ERK) and p65, activates the downstream MMP9 signalling pathway, inhibits MMP9 mRNA expression, inhibits protein activity, reduces type I collagen degradation, increases collagen secretion and promotes matrix remodelling and fibrosis in neonatal rat primary alveolar type II epithelial cells by overexpressing and silencing the HE4 gene.Conclusion: Through the ERK, MMP9 and TIMP1 signalling pathways, HE4 mediates the pathophysiological process of hyperoxia-induced lung damage in rats. Lung damage and lung basal remodelling are mediated by HE4 overexpression.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"378-396"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141616974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LncRNA GABPB1-AS1 is a potential target for the diagnosis of prostate cancer. LncRNA GABPB1-AS1 是诊断前列腺癌的潜在靶点。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-07-14 DOI: 10.1080/15257770.2024.2372315

Qi Chen, Yongsheng Pan, Xiufeng Yang, Hua Zhu, Bing Zheng, Longtao Ju

{"title":"LncRNA GABPB1-AS1 is a potential target for the diagnosis of prostate cancer.","authors":"Qi Chen, Yongsheng Pan, Xiufeng Yang, Hua Zhu, Bing Zheng, Longtao Ju","doi":"10.1080/15257770.2024.2372315","DOIUrl":"10.1080/15257770.2024.2372315","url":null,"abstract":"Background: Prostate cancer is an adverse tumor that occurs in the male reproductive system. The symptoms of patients in the early stage are not obvious and are generally difficult to detect.Aim: The aim of this study was to determine the regulation of lncRNA GABPB1-AS1 (GABPB1-AS1) on prostate cancer progression and explore the diagnostic potential of GABPB1-AS1.Methods: The contents of serum GABPB1-AS1 and miR-330-3p were examined by RT-qPCR assay. The functions of silencing GABPB1-AS1 and miR-330-3p inhibitor in prostate cancer cells were determined using transfection assay, CCK-8 assay and Transwell assay. The target of GABPB1-AS1 was predicted and verified at the molecular level by bioinformatics and luciferase reporter gene assay. The function of GABPB1-AS1 in prostate cancer diagnosis was evaluated via ROC method.Results: GABPB1-AS1 was upregulated in prostate cancer serum, which was associated with patients' Gleason score and TNM stage. Mechanistically, GABPB1-AS1 directly targeted miR-330-3p, and there was a negative correlation between them. Reduced levels of GABPB1-AS1 in cells after knockdown of GABPB1-AS1 resulted in decreased prostate cancer cell growth and activity, and these inhibitory effects were repaired by miR-330-3p inhibitor.Conclusion: The present study confirmed that GABPB1-AS1 was overexpressed in prostate cancer, and its sponge miR-330-3p may be an effective target for timely diagnosis of prostate cancer.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"587-597"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141616975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An improved synthesis of guanosine TNA phosphoramidite for oligonucleotide synthesis. 用于寡核苷酸合成的鸟苷 TNA 亚磷酰胺的改进合成法。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-06-21 DOI: 10.1080/15257770.2024.2369688

Biju Majumdar, Daisy Sarma, Erica M Lee, Noah A Setterholm, John C Chaput

引用次数: 0

Protective effect of FKBP12 on dextran sulfate sodium-induced ulcerative colitis in mice as a tacrolimus receptor. FKBP12 作为他克莫司受体对硫酸钠葡聚糖诱导的小鼠溃疡性结肠炎的保护作用

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-03-11 DOI: 10.1080/15257770.2024.2320817

Birong Wang, Tingzan Li, Liqin Xu, Yuxi Cai

{"title":"Protective effect of FKBP12 on dextran sulfate sodium-induced ulcerative colitis in mice as a tacrolimus receptor.","authors":"Birong Wang, Tingzan Li, Liqin Xu, Yuxi Cai","doi":"10.1080/15257770.2024.2320817","DOIUrl":"10.1080/15257770.2024.2320817","url":null,"abstract":"Ulcerative colitis (UC) is a multifactorial intestinal disease with a high incidence. In recent years, there has been an urgent need for pleiotropic drugs with a clear biosafety profile. Tacrolimus (TAC) is an immunosuppressant with stronger in vivo effects and better gastrointestinal absorption and is considered a potential treatment for UC. FKBP12 is a mediator of TAC immunosuppression; however, it is unclear whether it can participate in the development of UC in combination with TAC. The purpose of this study is to preliminarily validate the function of FKBP12 by establishing dextran sulfate sodium (DSS)-induced UC model and TAC treatment. The results revealed that TAC was effective in alleviating DSS-induced UC symptoms such as body weight and disease activity index (DAI). TAC significantly protects colonic tissue and attenuates DSS-induced histomorphological changes. In addition, FKBP12 is down-regulated in the intestinal tissue of DSS-induced UC mice and in serum samples of UC patients. In conclusion, our study revealed that FKBP12 may act as a TAC receptor to have anti-inflammatory and protective effects on DSS-induced UC in mice, which will provide a new option for the treatment of UC.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"206-221"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140102076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deprotection of N1-methyladenosine-containing RNA using triethylamine hydrogen fluoride. 使用三乙胺氟化氢对含 N1-甲基腺苷的 RNA 进行脱保护。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-05-12 DOI: 10.1080/15257770.2024.2353181

A Apostle, S Fang

{"title":"Deprotection of N1-methyladenosine-containing RNA using triethylamine hydrogen fluoride.","authors":"A Apostle, S Fang","doi":"10.1080/15257770.2024.2353181","DOIUrl":"10.1080/15257770.2024.2353181","url":null,"abstract":"The N1-methyladenosine (m1A) epigenetic modification exists in many RNAs and is related to many human diseases. Chemically synthesized RNAs containing the modification are required for projects aimed at studying biological processes, mechanisms, and pathogenesis related to m1A. Existing methods for the synthesis of m1A containing RNAs use tetrabutylammonium fluoride (TBAF) for the deprotection of the 2'-silyl protecting groups. Since TBAF is nonvolatile, and is relatively non-polar, its use in the desilylation of RNA requires repeated desalting, which is tedious and gives low yields. Here we report the use of the volatile and neat triethylamine hydrogen fluoride (TEA-HF) for desilylation of m1A RNA synthesis. We found that the method is much simpler, and-in our hands-give significantly higher yield of RNA. Two major concerns for m1A RNA synthesis are depurination and Dimroth rearrangement. HPLC and MALDI MS of the RNA indicated that depurination is not a problem for the new method. The absence of Dimroth rearrangement is proven by RNA digestion followed by HPLC analysis of the nucleosides.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"318-325"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140911755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Association between polymorphism at codon 469 of the ICAM-1 gene and Henoch-Schönlein purpura in an Iranian cohort. 伊朗队列中 ICAM-1 基因第 469 个密码子的多态性与白癜风之间的关系。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-04-27 DOI: 10.1080/15257770.2024.2334360

Shima Salehi, Amir Hozhabrpour, Somayeh Takrim Nojehdeh, Marzieh Mojbafan

引用次数: 0

Identification of CSNK1D and KLK6 as two common upregulated genes present in BRCA1 mutated triple-negative breast cancer and ovarian epithelial carcinoma. 确定 CSNK1D 和 KLK6 是 BRCA1 突变三阴性乳腺癌和卵巢上皮癌中两个常见的上调基因。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-05-23 DOI: 10.1080/15257770.2024.2357267

Fatima Lakis, Rita Ayoub, Wissam H Faour, Mohammad Makki, Hanane Yassine, Hussein Fayyad-Kazan, Fadi Abdel Sater

{"title":"Identification of CSNK1D and KLK6 as two common upregulated genes present in BRCA1 mutated triple-negative breast cancer and ovarian epithelial carcinoma.","authors":"Fatima Lakis, Rita Ayoub, Wissam H Faour, Mohammad Makki, Hanane Yassine, Hussein Fayyad-Kazan, Fadi Abdel Sater","doi":"10.1080/15257770.2024.2357267","DOIUrl":"10.1080/15257770.2024.2357267","url":null,"abstract":"Deficiency in the breast cancer type 1 (BRCA1) gene expression predisposes to triple-negative breast cancer (TNBC) and ovarian cancer (OC). We previously identified by Comparative Genomic Hybridization (CGH) array a gain in the 17q25.3 genomic region in 90% of the BRCA1 mutated TNBC tissues, where 17 genes were up-regulated. A second region (Chr19_45681759_54221324) was identified as the second most frequent gain in the BRCA1-mutated population and has not yet been described in the context of BRCA1 mutation. We thus aimed to validate the expression of the Casein kinase 1 delta (CSNK1D) gene of Chr17 in TNBC and OC cell lines and to investigate the expression of genes of Chr19 in TNBC cell lines and tissues as well as in OC cell lines. Expression level of the genes of the 17q25.3, 19q13.32,13.33 and 13.41 chromosomal regions was analyzed using RT-PCR in BRCA1 deficient TNBC and OC cell lines, as well as in 10 BRCA1-mutated TNBC tissues versus 10 wild type carriers. Our results revealed a significant upregulation of CSNK1D gene expression in BRCA1 deficient TNBC and OC cell lines when compared to control ones, and a significant aberration in the expression of the other six genes of Chr19 was observed. Interestingly, upregulation of kallikrein-related peptidase 6 (KLK6) was detected among the BRCA1 deficient TNBC (cell lines and tissues) and OC cell lines. In conclusion, our results suggested that CSNK1D and KLK6 expression levels could be very promising in the search for biomarkers for BRCA1 deficient TNBC and OC.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"554-567"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141088056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0